“I want to be clear that the United States is not in the business, in Egypt, of choosing winners and losers, even if we could, which, of course, we cannot,” Clinton said at the opening of the consulate.

US Secretary of State Hillary Clinton speaks during a flag-raising ceremony at the US Consulate General in the mediterranean city of Alexandria on July 15, 2012. Clinton is in Egypt to meet with the nation’s newly elected president. Photo AFP.

The protest appears to have been the result of suspicions that Washington had helped the Muslim Brotherhood win elections in Egypt in the wake of last year’s ouster of president Hosni Mubarak after 18 days of massive street protests.

During her two-day visit to Egypt, Clinton met with Egypt’s top military leaders, urging them to support a transition to civilian rule.

She also met with representatives of the country’s 10 million-strong Christian community, saying afterwards Washington was “committed to protecting and advancing the rights of all Egyptians: men and women, Muslim and Christian”.

Clinton’s meeting with Christian leaders comes after women and religious minorities expressed fears their rights could be rolled back following the post-revolution rise of the Islamists.

“I came to Cairo, in part, to send a very clear message that the United States supports the rights, the universal rights of all people,” Clinton said.

“We are going to look to any elected government to support inclusivity, to make sure that the talents of every Egyptian can be put to work in building a new future for this ancient and incredibly important country,” she said.

Egypt’s Christians have long complained of discrimination and marginalisation even under Mubarak’s secular regime.

Some Christian and secular activists had accused the United States of siding with Morsi during the election.

“There has been … that somehow the US has put its finger on the scale in favour of one side or another in this transition,” a state department official told reporters.

But Clinton “wanted … to dispel that notion and to make clear that only Egyptians can choose their leaders; that we have not supported any candidate, any party, and we will not,” the official said.